Finally the party reached the peak and entered the reactor. Sephiroth deduced that the reason why the Mt. Nibel's reactor was malfunctioning was because a section was broken in the mako purification tanks, although he initially didn't know why it broke.[1] However, it was discovered shortly thereafter that the reason it broke was because of what Hojo did with the purification tanks, where several human test subjects lay in tanks of Mako. It was also discovered that the remains of Jenova were sealed in a separate chamber. Troubled by the idea that he was created by the same process as the beings in the Mako tanks and the words of Genesis, Sephiroth returned to Nibelheim to investigate the matter using the abandoned Shinra mansion and the research notes in its basement.

With what he learned, Sephiroth was driven mad and razed Nibelheim before returning to Mt. Nibel to claim the remains of Jenova, who he had come to believe was his mother. Pursued by Zack, Cloud, Tifa and her father. Sephiroth fatally wounded Zack and Tifa's father and also flung Tifa down the industrial stairs, in the process of destroying the machinery in Jenova's chamber and claiming her head. Stabbed and heavily wounded by Cloud using Zack's Buster Sword, Sephiroth impaled Cloud with his sword, but Cloud was able to reverse the attack to pitch Sephiroth over the bridge and into the Lifestream, or down the shaft in the Jenova room, as depicted in Crisis Core.

During the events of Final Fantasy VII, Cloud Strife and his party cross through Mt. Nibel on during their worldwide journey after Sephiroth.

Like in Nibelheim, the track "On That Day, 5 Years Ago" (5年前のあの日 Gonen Mae no ano Hi) continues to play in Mt. Nibel. When the party returns to Mt. Nibel, "Under the Rotting Pizza" (腐ったピザの下で Kusatta Piza no Shita De) plays as the background music.
In Crisis core - Final Fantasy VII March on the frontier plays as the backgroung theme , whereas inside the reactar The Skyscraper of Iron and Steel plays.